LAMMPS (13 Oct 2016)
# sample LAMMPS input script for viscosity of 2d LJ liquid
# Muller-Plathe via fix viscosity

# settings

variable	x equal 20
variable	y equal 20

variable	rho equal 0.6
variable        t equal 1.0
variable	rc equal 2.5

# problem setup

units		lj
dimension	2
atom_style	atomic
neigh_modify	delay 0 every 1

lattice         sq2 ${rho}
lattice         sq2 0.6
Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
region          simbox block 0 $x 0 $y -0.1 0.1
region          simbox block 0 20 0 $y -0.1 0.1
region          simbox block 0 20 0 20 -0.1 0.1
create_box      1 simbox
Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
  1 by 1 by 1 MPI processor grid
create_atoms    1 box
Created 800 atoms

pair_style      lj/cut ${rc}
pair_style      lj/cut 2.5
pair_coeff      * * 1 1

mass            * 1.0
velocity        all create $t 97287
velocity        all create 1 97287

fix             1 all nve
fix	        2 all langevin $t $t 0.1 498094
fix	        2 all langevin 1 $t 0.1 498094
fix	        2 all langevin 1 1 0.1 498094
fix	        3 all enforce2d

# equilibration run

thermo          1000
run	        5000
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4 -> bins = 27 27 1
Memory usage per processor = 2.47956 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            1     -1.56492            0     -0.56617    -1.535262 
    1000   0.95906897    -1.571142            0  -0.61327189   0.82593948 
    2000    1.0164992   -1.6006146            0  -0.58538603   0.88642098 
    3000    1.0429232   -1.5801639            0  -0.53854441     1.157286 
    4000    1.0955206   -1.6156387            0  -0.52148756   0.94410568 
    5000    0.9411767   -1.6155061            0  -0.67550589   0.79353873 
Loop time of 0.860626 on 1 procs for 5000 steps with 800 atoms

Performance: 2509801.057 tau/day, 5809.725 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.48372    | 0.48372    | 0.48372    |   0.0 | 56.21
Neigh   | 0.11227    | 0.11227    | 0.11227    |   0.0 | 13.05
Comm    | 0.014462   | 0.014462   | 0.014462   |   0.0 |  1.68
Output  | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 |   0.0 |  0.01
Modify  | 0.22682    | 0.22682    | 0.22682    |   0.0 | 26.35
Other   |            | 0.02332    |            |       |  2.71

Nlocal:    800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    5583 ave 5583 max 5583 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 5583
Ave neighs/atom = 6.97875
Neighbor list builds = 551
Dangerous builds = 0

unfix		2

# turn on Muller-Plathe driving force and equilibrate some more

velocity	all scale $t
velocity	all scale 1

fix		4 all viscosity 100 x y 20

compute         layers all chunk/atom bin/1d y center 0.05 units reduced
fix		5 all ave/chunk 20 50 1000 layers vx file profile.mp.2d

# equilibration run

variable	dVx equal f_5[11][3]-f_5[1][3]

thermo          1000
thermo_style	custom step temp epair etotal press f_4 v_dVx
run		20000
Memory usage per processor = 2.72975 Mbytes
Step Temp E_pair TotEng Press f_4 v_dVx 
    5000            1   -1.6155061  -0.61675613   0.82878859            0            0 
    6000   0.99205567   -1.6073706  -0.61655497   0.80256133   -40.441513   0.49442509 
    7000   0.98076638   -1.5968401   -0.6172997   0.93482147   -74.701801   0.81873121 
    8000   0.99350602   -1.6093282  -0.61706408    1.0032966   -108.00017    1.0369989 
    9000    1.0130047   -1.6282491  -0.61651065   0.89200717   -133.06372    1.1272589 
   10000    1.0016704   -1.6170906  -0.61667231    1.0115493   -164.86086    1.1885507 
   11000   0.99991137   -1.6160496  -0.61738807   0.95811584   -190.62317    1.3389184 
   12000   0.96344622   -1.5793561   -0.6171142    1.0416296   -221.40727    1.2111221 
   13000   0.98692912   -1.6022586  -0.61656313    0.9183328    -250.6677    1.4028399 
   14000    1.0007815   -1.6169097  -0.61737918   0.85210278    -280.3907    1.3446354 
   15000   0.99742966   -1.6127263   -0.6165434   0.81573578   -308.44839    1.4070968 
   16000    0.9955551   -1.6105533  -0.61624268   0.88385735   -336.00553    1.3867041 
   17000   0.98598927   -1.6016934  -0.61693666    1.0601453   -363.09101    1.3716356 
   18000    0.9827155   -1.5988654  -0.61737831   0.97685532   -391.14488    1.2259196 
   19000   0.96881647   -1.5839283   -0.6163228    0.9709967   -418.82566    1.2683115 
   20000    1.0265924   -1.6430234  -0.61771432   0.66156099   -448.12442    1.0964927 
   21000    1.0001781   -1.6169267  -0.61799878   0.94637366   -477.11852    1.3532793 
   22000    1.0014617   -1.6170345  -0.61682461   0.89064741   -503.16769    1.2348173 
   23000   0.98723824   -1.6033256  -0.61732136   0.95636024   -533.04118     1.309259 
   24000   0.97802015   -1.5945708  -0.61777318    1.1331272   -560.01862    1.3396892 
   25000   0.98672719   -1.6025172  -0.61702339    1.0225572   -585.97779    1.5256433 
Loop time of 2.83606 on 1 procs for 20000 steps with 800 atoms

Performance: 3046484.279 tau/day, 7052.047 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.9431     | 1.9431     | 1.9431     |   0.0 | 68.52
Neigh   | 0.48329    | 0.48329    | 0.48329    |   0.0 | 17.04
Comm    | 0.061027   | 0.061027   | 0.061027   |   0.0 |  2.15
Output  | 0.00022459 | 0.00022459 | 0.00022459 |   0.0 |  0.01
Modify  | 0.25409    | 0.25409    | 0.25409    |   0.0 |  8.96
Other   |            | 0.09429    |            |       |  3.32

Nlocal:    800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    258 ave 258 max 258 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    5583 ave 5583 max 5583 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 5583
Ave neighs/atom = 6.97875
Neighbor list builds = 2363
Dangerous builds = 0

# data gathering run
# reset fix viscosity to zero flux accumulation

unfix		4
fix		4 all viscosity 100 x y 20

variable	visc equal -(f_4/(2*(step*0.005-125)*lx+1.0e-10))/(v_dVx/(ly/2))
fix		vave all ave/time 1000 1 1000 v_visc ave running start 26000

thermo_style	custom step temp f_4 v_dVx v_visc f_vave

# only need to run for 10000 steps to make a good 100-frame movie

#dump	        1 all custom 100 dump.mp.2d id type x y z vx

#dump		2 all image 100 image.*.jpg vx type zoom 1.6 adiam 1.2
#dump_modify	2 pad 5 amap -0.7 0.7 ca 0.0 2 min blue max red

run	        50000
Memory usage per processor = 2.73047 Mbytes
Step Temp f_4 v_dVx v_visc f_vave 
   25000   0.98672719            0    1.5256433           -0            0 
   26000   0.98401533   -25.559065    1.3332094   0.95855405   0.47927702 
   27000   0.99050741    -53.17367    1.3419843   0.99057919   0.64971108 
   28000   0.98153807   -83.114662    1.1794868    1.1744467   0.78089498 
   29000    1.0204966   -110.22215    1.3360187    1.0312556   0.83096712 
   30000   0.99625662   -133.82368    1.5944344   0.83931757   0.83235886 
   31000    1.0151551    -158.7453    1.5031209   0.88008718   0.83917719 
   32000   0.98303358   -184.40723    1.4652847   0.89893417   0.84664681 
   33000   0.99939957   -210.86096    1.3135851    1.0032703   0.86404943 
   34000   0.96853185   -235.91032    1.3291636   0.98604334   0.87624882 
   35000    1.0054026   -267.07311    1.4280769   0.93507957   0.88159707 
   36000   0.97047213   -290.05846    1.4030844   0.93967798   0.88643714 
   37000   0.99339602   -317.88469    1.3395274   0.98879613   0.89431091 
   38000    1.0095839   -339.72956    1.5081424   0.86639838   0.89231716 
   39000     1.033396   -365.46114    1.4202859   0.91898285   0.89409487 
   40000    1.0069829   -391.35939    1.4315171   0.91129289   0.89516975 
   41000    1.0145044   -417.94062    1.5126265   0.86344149   0.89330338 
   42000   0.99701243   -442.43582    1.3830081   0.94090688   0.89594802 
   43000     1.011832   -466.04588     1.514607    0.8547246   0.89377837 
   44000     1.016323   -494.28239    1.4459083   0.89960277   0.89406959 
   45000    1.0048565   -518.02843    1.4397428   0.89951556   0.89432892 
   46000   0.99726082   -546.29139    1.2399161    1.0490176   0.90136022 
   47000    0.9817128    -579.0368    1.2816209     1.026819   0.90681495 
   48000   0.99883406   -606.89944    1.3508577   0.97667325   0.90972571 
   49000    1.0327324   -639.80418     1.227321    1.0860446   0.91677847 
   50000   0.99442217   -668.69881    1.1824503    1.1310391   0.92501927 
   51000   0.99412485   -695.56436    1.3288051    1.0066366   0.92804213 
   52000    1.0368955   -724.06214    1.2921091    1.0377265   0.93195943 
   53000      1.02122   -749.03672    1.5201682      0.87988   0.93016359 
   54000    1.0304794   -772.90678    1.3994802    0.9522092   0.93089844 
   55000    1.0150735   -800.69744    1.2226831    1.0914486   0.93607748 
   56000    1.0066993   -830.92913    1.4581021   0.91914572   0.93554836 
   57000   0.99054006   -858.94251    1.3736656   0.97701919   0.93680505 
   58000    1.0300499   -881.47715    1.5995216   0.83498179   0.93381025 
   59000   0.99187983   -909.58612    1.4692824   0.91039454   0.93314123 
   60000    1.0116153   -936.80603     1.372993    0.9747277   0.93429641 
   61000   0.98778111   -966.36841    1.3911445    0.9648015   0.93512087 
   62000   0.97796351   -996.15306    1.2818309    1.0501797   0.93814874 
   63000    1.0241007   -1026.5146    1.3364909    1.0106145   0.94000683 
   64000    1.0447876   -1051.1752    1.4339955   0.93979412   0.94000152 
   65000     1.013822   -1078.5189    1.5730359   0.85703609   0.93797797 
   66000    1.0003625   -1104.7839    1.4374578   0.93727789    0.9379613 
   67000    1.0411074   -1132.5569    1.4426372   0.93459539   0.93788302 
   68000    1.0005746   -1162.5849    1.2729721     1.061958   0.94070291 
   69000    1.0032978   -1189.5061    1.4109135   0.95803997   0.94108818 
   70000     1.003145   -1215.7498    1.4255228   0.94760543   0.94122986 
   71000    1.0216551   -1244.4852    1.1329731    1.1939394   0.94660666 
   72000   0.96169183   -1272.9346    1.1024076    1.2283893   0.95247713 
   73000   0.96956712   -1298.3657    1.3689638   0.98794738   0.95320101 
   74000    1.0081417   -1327.5255    1.3483851    1.0046224   0.95422944 
   75000    1.0315254   -1357.3275    1.4937254    0.9086861   0.95333643 
Loop time of 7.08146 on 1 procs for 50000 steps with 800 atoms

Performance: 3050218.869 tau/day, 7060.692 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.8558     | 4.8558     | 4.8558     |   0.0 | 68.57
Neigh   | 1.2027     | 1.2027     | 1.2027     |   0.0 | 16.98
Comm    | 0.15117    | 0.15117    | 0.15117    |   0.0 |  2.13
Output  | 0.00069261 | 0.00069261 | 0.00069261 |   0.0 |  0.01
Modify  | 0.63608    | 0.63608    | 0.63608    |   0.0 |  8.98
Other   |            | 0.235      |            |       |  3.32

Nlocal:    800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    273 ave 273 max 273 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    5612 ave 5612 max 5612 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 5612
Ave neighs/atom = 7.015
Neighbor list builds = 5873
Dangerous builds = 0
Total wall time: 0:00:10
